Ophthalmic Bioengineering. Review

This article published the materials of the round table “Bioengineering in ophthalmology” (OphthalmicBioengineering), held on May 13, 2021 as part of the international conference Ural Symposium on Biomedical Engineering, Radioelectronics and Information Technology (USBEREIT). USBEREIT is held under the auspices of the IEEE Engineering in Medicine and Biology Society. The article presents reports on: metrological aspects of registration of tonometric and electrophysiological signals in ophthalmic diagnostics; approaches to modeling the processes of pulse blood filling of the eye with the determination of hemodynamic parameters; retinotoxicity based on electrophysiological signals; analysis of electrophysiological signals in the frequency-time domain and its application in clinical practice; extraction and analysis of specialized data obtained from the electrophysiological medical device; as well as diagnosing retinal diseases based on optical coherence tomography using machine learning. © 2023 Ophthalmology Publishing Group. All rights reserved

Deep learning-based video stream reconstruction in mass-production diffractive optical systems

Возможность существенно снизить массу и стоимость систем технического зрения привела к появлению большого числа работ, посвященных разработке новых оптических схем на основе дифракционной оптики и новых подходов к реконструкции получаемых изображений. Получаемые системы демонстрируют достаточное для прикладных систем технического зрения качество изображений. Однако при создании таких прикладных систем возможны источники дополнительных потерь качества получаемого видеопотока. В настоящей работе исследовано влияние на итоговое качество реконструируемого видеопотока таких факторов, как ограничения технологии массового производства дифракционной оптики, артефактов сжатия видеопотока с потерями, а также особенностей нейросетевого подхода к реконструкции. Предложена сквозная нейросетевая технология реконструкции изображений, позволяющая компенсировать дополнительные факторы потери качества и получить итоговый видеопоток с качеством, достаточным для решения прикладных задач технического зрения. Many recent studies have focused on developing image reconstruction algorithms in optical systems based on flat optics. These studies demonstrate the feasibility of applying a combination of flat optics and the reconstruction algorithms in real vision systems. However, additional causes of quality loss have been encountered in the development of such systems. This study investigates the influence on the reconstructed image quality of such factors as limitations of mass production technology for diffractive optics, lossy video stream compression artifacts, and specificities of a neural network approach to image reconstruction. The paper offers an end-to-end deep learning-based image reconstruction framework to compensate for the additional factors of quality losing. It provides the image reconstruction quality sufficient for applied vision systems.Теоретическая часть работы и разработка нейросетевых моделей выполнена при поддержке гранта РНФ 20-69-47110, экспериментальная часть выполнена при поддержке грантов РФФИ № 18-07-01390-А, а также в рамках государственного задания ИСОИ РАН – филиала Федерального научно-исследовательского центра «Кристаллография и фотоника» РАН (соглашение № 007-ГЗ/Ч3363/26)

Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes

With the existence of large publicly available plant gene expression data sets, many groups have undertaken data analyses to construct gene coexpression networks and functionally annotate genes. Often, a large compendium of unrelated or condition-independent expression data is used to construct gene networks. Condition-dependent expression experiments consisting of well-defined conditions/treatments have also been used to create coexpression networks to help examine particular biological processes. Gene networks derived from either condition-dependent or condition-independent data can be difficult to interpret if a large number of genes and connections are present. However, algorithms exist to identify modules of highly connected and biologically relevant genes within coexpression networks. In this study, we have used publicly available rice (Oryza sativa) gene expression data to create gene coexpression networks using both condition-dependent and condition-independent data and have identified gene modules within these networks using the Weighted Gene Coexpression Network Analysis method. We compared the number of genes assigned to modules and the biological interpretability of gene coexpression modules to assess the utility of condition-dependent and condition-independent gene coexpression networks. For the purpose of providing functional annotation to rice genes, we found that gene modules identified by coexpression analysis of condition-dependent gene expression experiments to be more useful than gene modules identified by analysis of a condition-independent data set. We have incorporated our results into the MSU Rice Genome Annotation Project database as additional expression-based annotation for 13,537 genes, 2,980 of which lack a functional annotation description. These results provide two new types of functional annotation for our database. Genes in modules are now associated with groups of genes that constitute a collective functional annotation of those modules. Additionally, the expression patterns of genes across the treatments/conditions of an expression experiment comprise a second form of useful annotation

DYX1C1 is required for axonemal dynein assembly and ciliary motility

DYX1C1 has been associated with dyslexia and neuronal migration in the developing neocortex. Unexpectedly, we found that deleting exons 2–4 of Dyx1c1 in mice caused a phenotype resembling primary ciliary dyskinesia (PCD), a disorder characterized by chronic airway disease, laterality defects and male infertility. This phenotype was confirmed independently in mice with a Dyx1c1 c.T2A start-codon mutation recovered from an N-ethyl-N-nitrosourea (ENU) mutagenesis screen. Morpholinos targeting dyx1c1 in zebrafish also caused laterality and ciliary motility defects. In humans, we identified recessive loss-of-function DYX1C1 mutations in 12 individuals with PCD. Ultrastructural and immunofluorescence analyses of DYX1C1-mutant motile cilia in mice and humans showed disruptions of outer and inner dynein arms (ODAs and IDAs, respectively). DYX1C1 localizes to the cytoplasm of respiratory epithelial cells, its interactome is enriched for molecular chaperones, and it interacts with the cytoplasmic ODA and IDA assembly factor DNAAF2 (KTU). Thus, we propose that DYX1C1 is a newly identified dynein axonemal assembly factor (DNAAF4)

High-temperature kinetic properties of Fe-Ge solid solutions

Temperature and concentrational dependences of the electrical resistivity ρ, thermoelectric power S, and thermal diffusivity a of solid solutions of Ge in Fe were studied at high temperatures. The a(T) dependences of the alloys with 0.0, 0.31, 0.8, 1.08, and 2.6 at. % Ge exhibit anomalies near the temperature of the β-γ transformation; in this case, changes in the spectra of inner electron levels are observed. The high-temperature kinetic properties of solid solutions of Ge in Fe are close to those of metals and, therefore, the ρ(T) and a(T) dependences can be explained using the model of two-band conduction